Hough's article that's linked in the OP seems to be the classical definition of linkbait to me: outrageous claim backed up with little than simplistic reasoning. It does not even have anecdotal evidence, e.g. I talked to X's founder and he told me that YC or Techstars hurt their startup in so and so way.

Some particular points:

* "Startup incubators don’t guarantee that your startup will be successful when you leave the program after three months — although the big profile programs do hint at success through association." If you get involved with an incubator thinking it's a guarantee for success you are naive indeed. And where exactly does, say, YC "hint at success".

* "Since 2005, Y Combinator has funded 460 startups with only a handful of big wins." This is the meat of the article. Since so few YC companies are successful, the YC experience must be hurting the applicants. The ratio "handful" to 460 must be compared to successful startup which didn't participate in an incubator to all start ups founded since 2005. BTW, for an analysis of "handful" see this discussion: http://news.ycombinator.com/item?id=2608440. Big hands indeed!

* The only two points that are of importance, I think, are the uncontrolled publicity and relocation stress. Relocation is absolutely necessary, to cut you off from you usual surroundings. It's similar to the monks's shaving off their hair when they start their new life: a big step to show, especially to yourself, that you are starting something new. The uncontrolled publicity is a problem, but this dogs many a Kickstarter company, too.

I've never done a YC round and am not a YC fanboy (in particular I'm worried about the uncontrolled publicity that YC itself is getting and its increased class size may dilute it.) but from what I read from HN over the years it seems to be a seminal experience.